FIELDimageR pipeline:
Image analysis applied to plant breeding

Introduction

Plant Breeding

Images can be used in plant breeding to draw inference about many traits:

  • Geometric traits (i.e. plant height, leaf area index, lodging, crop canopy cover)
  • Canopy spectral texture (spectral features)
  • Physiological traits (i.e., chlorophyll, biomass, pigment content, photosynthesis)
  • Abiotic/biotic stress indicators (i.e., stomatal conductance, canopy temperature difference, leaf water potential, senescence index)
  • Nutrients (nitrogen concentration, protein content)
  • Yield

FIELDimageR

FIELDimageR is a R package to analyze images from plant breeding programs, and allows to:

  • Crop the image
  • Remove soil effect
  • Build vegetation indices
  • Rotate the image
  • Build the plot shapefile
  • Extract information for each plot
  • Evaluate stand count, canopy percentage, and plant height

FIELDimageR pipeline

1) Example 01

Remote sensing (Potato Breeding)

Jeffrey Endelman and Filipe Matias (UW-Madison)

Orthomosaic using Open Drone Map (ODM)

Follow the OpenDroneMap’s documentation according to your operating system (Windows, macOS or Linux) to install WebODM.

Start WebODM and +Add Project to upload the RGB images from the Tropical Forage Breeding - Embrapa Beef Cattle:

After the running process ‘completed’, download the odm_orthophoto.tif and dsm.tif to upload in R. Then follow the pipeline of FIELDimageR.

Data extraction (R/FIELDimageR)

Required packages

  • Evaluating each trial per time:

  • Estimation of plant height using a high throughput phenotyping platform. (Donwload: dsm.tif)

  • Heritability

2) Example 02

Evaluating disease damage (Tomato Breeding)

Fernando Piotto and Jéssica Nogueira (ESALQ/USP)

  • Donwload: EX2.zip
  • Pictures of 10 genotypes with Xanthomonas perforans

* Parallel

Reference

Matias, F.I. (2019). FIELDimageR Pipeline (tutorial). https://github.com/filipematias23/FIELDimageR

Matias, F.I.; Caraza-Harter, M.; Endelman, J.B. (2020). FIELDimageR: A R Package to Analyze Orthomosaic Images from Agricultural Field Trials. The Plant Phenome Journal. DOI:10.1002/ppj2.20005

Filipe Matias
Department of Horticulture
University of Wisconsin-Madison

2020-08-12